changed reporting in ccode to only report those who are found to be chimeric by all...

[mothur.git] / decalc.cpp

diff --git a/decalc.cpp b/decalc.cpp
index 2d60899e7c9f9526d531336fc1159f65ebed05bc..b2e8be61f8df0aff52753058532a3ef42c6b6f0f 100644 (file)
--- a/decalc.cpp
+++ b/decalc.cpp
@@ -21,12 +21,17 @@ void DeCalculator::setMask(string m) {
                        for (int i = 0; i < seqMask.length(); i++) {
                                if (isalpha(seqMask[i])) {
                                        h.insert(i);
-                                       maskMap[i] = count;
+                                       maskMap[count] = i;
+                                       count++;
+                                       
                                }
-                               count++;
                        }
                }else {
-                       for (int i = 0; i < alignLength; i++) {   h.insert(i);  }
+                       for (int i = 0; i < alignLength; i++) {   
+                               h.insert(i); 
+                               maskMap[count] = i;
+                               count++;
+                       }
                }
        }
        catch(exception& e) {